#ubiquitin

[humancelltournament]

Propaganda!

Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ubiquitously. The addition of ubiquitin to a substrate protein is called ubiquitylation (or ubiquitination or ubiquitinylation). Ubiquitylation affects proteins in many ways: it can mark them for degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein interactions.[4][5][6] Ubiquitylation involves three main steps: activation, conjugation, and ligation, performed by ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively.

Dopamine (DA, a contraction of 3,4-dihydroxyphenethylamine) is a neuromodulatory molecule that plays several important roles in cells. It is an organic chemical of the catecholamine and phenethylamine families. Dopamine constitutes about 80% of the catecholamine content in the brain. It is an amine synthesized by removing a carboxyl group from a molecule of its precursor chemical, L-DOPA, which is synthesized in the brain and kidneys. In the brain, dopamine functions as a neurotransmitter—a chemical released by neurons (nerve cells) to send signals to other nerve cells. Neurotransmitters are synthesized in specific regions of the brain, but affect many regions systemically. The brain includes several distinct dopamine pathways, one of which plays a major role in the motivational component of reward-motivated behavior.

[nerdwelt]

Proteinfabriken zum Laufen bringen – Wie deubiquitinierende Enzyme neben Fubi-Proteasen stehen

Forscher des Max-Planck-Instituts für molekulare Physiologie haben neue Erkenntnisse über die Rolle von Fubi-Proteasen bei der Reifung von Ribosomen gewonnen. Fubi ist eine Ubiquitin-ähnliche Modifikatorproteinfamilie, die bisher wenig erforscht wurde. Die Wissenschaftler haben zwei deubiquitinierende Enzyme identifiziert, die als Fubi-Proteasen fungieren und die Trennung von Fubi von ribosomalem…

[whats-in-a-sentence]

JA acts through a conserved ubiquitin ligase-based signaling mechanism that bears close resemblance to those described for auxin and gibberellin (Figure 23.19). (...) Two additional proteins and two histone deacetylase enzymes (HDA6 and HDA19) act as co-repressors asking with the JAZ-COI1 complex and are instrumental in maintaining the chromatin in an inactive state (see Figure 23.19). The binding of JA-Ile to the JAZ-COI1 co-receptors leads to the ubiquitination of JAZ by the SCF^(COI1-JA-Ile) complex, followed by JAZ degradation via the 26S proteasome (see Figure 23.19).

"Plant Physiology and Development" int'l 6e - Taiz, L., Zeiger, E., Møller, I.M., Murphy, A.

[tenth-sentence]

The plant hormones jasmonate and gibberellin also promote the interaction between an F-box protein of a SCF ubiquitin E3 ligase and its transcriptional repressor target proteins (Figure 15.34B and C).

"Plant Physiology and Development" int'l 6e - Taiz, L., Zeiger, E., Møller, I.M., Murphy, A.

[chinesegreenteagoldentriangle]

Mechanism of EGCG binding to p53 revealed: Polyphenolic compounds in green tea may enhance anti-tumor activity by stabilizing p53.

A new study has found that epigallocatechin gallate (EGCG), a polyphenolic compound found in green tea, can induce apoptosis in cancer cells, but its potential molecular mechanisms are not well understood. Recently, a team led by Chunyu Wang at Rensselaer Polytechnic Institute (with China Agricultural University as the first author's affiliation and Jing Zhao as the first author of the paper) published a study in Nature Communications titled "EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction". The study used SPR and NMR to report the direct interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the main binding site (KD = 4 ± 2 μM). Large-scale atomic simulations (>100 μs), SAXS, and AUC showed that the EGCG-NTD interaction is dynamic, with EGCG leading to a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupted the interaction between p53 and its regulatory E3 ligase MDM2 and inhibited MDM2-mediated ubiquitination of p53 in vitro, potentially stabilizing p53's anti-tumor activity. Overall, this study provides insights into the anti-cancer mechanism of EGCG and identifies the p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.

In recent years, diet-based cancer prevention and treatment have received considerable attention. Green tea is a popular beverage worldwide and has been reported to have inhibitory effects on various types of cancers, such as breast cancer, lung cancer, prostate cancer, and colon cancer. Most of the chemopreventive effects of green tea on cancer are attributed to polyphenolic compounds, with epigallocatechin-3-gallate (EGCG) being the most important. EGCG accounts for 50-80% of the catechins in green tea. A cup of brewed green tea (240 mL) contains 200-300 mg of EGCG. A serum concentration of 0.1-1 μM EGCG can be achieved by drinking a cup of green tea or taking an EGCG tablet. The anticancer effects of EGCG have been confirmed in epidemiological, cell culture and animal studies, as well as clinical trials.

A 10-year prospective study by Nakachi and Imai reported that people who drink more than 10 cups of green tea per day have a lower risk of cancer compared to those who drink less than 3 cups per day. Recently, Shin et al. found in a randomized clinical trial in Korea that green tea extract can reduce the recurrence rate of colorectal adenomas by 44.2%. In vitro, EGCG has been shown to promote growth arrest and induce apoptosis in a variety of human cancer cell lines, including prostate cancer cells, epidermoid carcinoma cells, bladder cancer cells, and colon cancer cells.

In mice, oral administration of green tea or intravenous injection of purified EGCG can inhibit angiogenesis and suppress the growth of solid tumors. At the molecular level, EGCG has been shown to interact with cancer-associated proteins, such as glucose-regulated protein 78 (GRP78) and Ras-GTPase-activating protein SH3 domain-binding protein 1 (G3BP1), with an affinity of approximately μM.

In EGCG-induced apoptosis and growth arrest, p53 plays an important role. p53, often referred to as the "guardian of the genome," is a critical tumor suppressor that is mutated in over 50% of human cancers. p53 promotes cell cycle arrest or apoptosis as a response to cellular stress stimuli such as oxidative stress, oncogene activation, and DNA damage. As a transcription factor, p53 is tightly regulated and has a short half-life. p53 protein is typically maintained at low levels in healthy mammalian cells through continuous ubiquitination and subsequent degradation.

Under cellular stress, ubiquitination of p53 is inhibited, and p53 is stabilized. Then p53 accumulates in the cell nucleus and activates the expression of target genes, thereby triggering cell cycle arrest, apoptosis, and DNA repair processes. In addition to serving as a transcription factor, p53 can also be translocated to the cytoplasm or mitochondria. p53 directly interacts with anti-apoptotic proteins such as Bax and Bcl2 to induce apoptosis and also participates in the anti-aging effects of EGCG.

Full-length p53 consists of an N-terminal domain (NTD), a DNA-binding domain (DBD), a tetramerization domain (TET), and a C-terminal regulatory domain (REG). The NTD is further divided into two transcription activation domains (TAD1 and TAD2) and a proline-rich domain (PRD). The NTD is an intrinsically disordered protein (IDP) that interacts with many proteins and serves as a hub for cellular signal transduction. The NTD is not only necessary for transactivation but also interacts with MDM2 to mediate the ubiquitination and degradation of p53.

Independent of ubiquitination, MDM2 also inhibits transcription by preventing the general transcription factors from binding to the NTD. The apoptotic effect of EGCG on human cancer cells is related to its interference with MDM2-mediated ubiquitination of p53. It has been reported that EGCG can also stabilize p53 and increase the phosphorylation of critical serine residues. In a recent study, EGCG was identified as an inhibitor of the p53-MDM2 interaction from a library of 2,295 plant chemicals. However, the molecular mechanism by which EGCG disrupts the MDM2-p53 interaction is not yet clear.

In this work, direct binding between EGCG and p53 mediated by the NTD of p53 was demonstrated. The study suggests that the EGCG-p53 interaction disrupts the MDM2-p53 interaction and inhibits the ubiquitination of p53, potentially stabilizing p53's anti-tumor activity and providing a structural mechanism for the anti-cancer effects of EGCG.

[girlactionfigure]

1 Nobel Prize in Chemistry - The Development of Multiscale Models for Complex Chemical Systems

2 Nobel Prize in Chemistry - Quasiperiodic Crystals

3 Nobel Prize in Chemistry - Decoding the Structure and The Function of The Ribosome

4 Nobel Prize in Economic Sciences - Repeated Games

5 Nobel Prize in Chemistry – Ubiquitin, Deciding the Fate of Defective Proteins in Living Cells

6 Nobel Prize in Economics - Human Judgment and Decision-Making Under Uncertainty

7 Fields Medal Award in Mathematics

8 Turing Award - Machine Reasoning Under Uncertainty

9 Turing Award - Nondeterministic Decision-Making

10 Turing Award - The Development of Interactive Zero-Knowledge Proofs

11 Turing Award - Developing New Tools for Systems Verification

12 Vine Seeds Discovered from The Byzantine Period

13 The World’s Most Ancient Hebrew Inscription

14 Ancient Golden Treasure Found at Foot of Temple Mount

15 Sniffphone - Mobile Disease Diagnostics

16 Discovering the Gene Responsible for Fingerprints Formation

17 Pillcam - For Diagnosing and Monitoring Diseases in The Digestive System

18 Technological Application of The Molecular Recognition and Assembly Mechanisms Behind Degenerative Disorders

19 Exelon – A Drug for The Treatment of Dementia

20 Azilect - Drug for Parkinson’s Disease

21 Nano Ghosts - A “Magic Bullet” For Fighting Cancer

22 Doxil (Caelyx) For Cancer Treatment

23 The Genetics of Hearing

24 Copaxone - Drug for The Treatment of Multiple Sclerosis

25 Preserving the Dead Sea Scrolls

26 Developing the Biotechnologies of Valuable Products from Red Marine Microalgae

27 A New Method for Recruiting Immune Cells to Fight Cancer

28 Study of Bacterial Mechanisms for Coping with Temperature Change

29 Steering with The Bats 30 Transmitting Voice Conversations Via the Internet

31 Rewalk – An Exoskeleton That Enables Paraplegics to Walk Again

32 Intelligent Computer Systems

33 Muon Detectors in The World's Largest Scientific Experiment

34 Renaissance Robot for Spine and Brain Surgery

35 Mobileye Accident Prevention System

36 Firewall for Computer Network Security

37 Waze – Outsmarting Traffic, Together

38 Diskonkey - USB Flash Drive

39 Venμs Environmental Research Satellite

40 Iron Dome – Rocket and Mortar Air Defense System

41 Gridon - Preventing Power Outages in High Voltage Grids

42 The First Israeli Nanosatellite

43 Intel's New Generation Processors

44 Electroink - The World’s First Electronic Ink for Commercial Printing

45 Development of A Commercial Membrane for Desalination

46 Developing Modern Wine from Vines of The Bible

47 New Varieties of Seedless Grapes

48 Long-Keeping Regular and Cherry Tomatoes

49 Adapting Citrus Cultivation to Desert Conditions

50 Rhopalaea Idoneta - A New Ascidian Species from The Gulf of Eilat

51 Life in The Dead Sea - Various Fungi Discovered in The Brine

52 Drip Technology - The Irrigation Method That Revolutionized Agriculture

53 Repair of Heart Tissues from Algae

54 Proof of The Existence of Imaginary Particles, Which Could Be Used in Quantum Computers

55 Flying in Peace with The Birds

56 Self-Organization of Bacteria Colonies Sheds Light on The Behaviour of Cancer Cells

57 The First Israeli Astronaut, Colonel Ilan Ramon

58 Dr. Chaim Weizmann - Scientist and Statesman, The First President of Israel, One of The Founders of The Modern Field of Biotechnology

59 Aaron Aaronsohn Botanist, Agronomist, Entrepreneur, Zionist Leader, and Head of The Nili Underground Organization

60 Albert Einstein - Founding Father of The Theory of Relativity, Co-Founder of the Hebrew University in Jerusalem

61 Maimonides - Doctor and Philosopher

Source

@TheMossadIL

[hellsite-proteins]

oh you want cursed biochem acronyms? good god i���ve got some absolute Bricks to share.

piRNA - PIWI interacting RNA

PIWI and RNA are also both acronyms

PIWI - p-element-induced wimpy testis

yes they’re nesting acronyms now. yes i hate it.

UHRF1 - "ubiquitin-like, containing PHD and RING finger domains, 1"

once again PHD and RING are both acronyms. STOP NESTING ACRONYMS

PHD - plant homeodomain

RING - really interesting new gene

reading papers for genetics/biochem courses is like. ah how many random sequences of letters can we cram in here before people start calling bullshit. and apparently? it’s a lot.

today i googled GPS looking for 'global protein stability', and was completely shocked when i was reminded that there is a much more common use for that acronym. please share any more cursed acronyms you know in the notes!

letter sequence in this ask matching protein-coding amino acids:

hywantcrsedichemacrnymsgdgdivegtsmeaslterickstsharepiRNAPIWIinteractingRNAPIWIandRNAarealsthacrnymsPIWIpelementindcedwimpytestisyestheyrenestingacrnymsnwyesihateitHRFiqitinlikecntainingPHDandRINGfingerdmainsnceagainPHDandRINGarethacrnymsSTPNESTINGACRNYMSPHDplanthmedmainRINGreallyinterestingnewgenereadingpapersfrgeneticsichemcrsesislikeahhwmanyrandmseqencesfletterscanwecraminhereefrepeplestartcallingllshitandapparentlyitsalt

protein guy analysis:

this structure does a wonderful job illustrating the difference between secondary and tertiary structure. there is a decent amount of secondary structure, with lots of alpha helices of widely varying lengths. however, they do not actually come together to make anything. that is why, when you look at the surface, it is more holes than protein. it seems that unnatural, random proteins with a hydrophobic core may be more likely to aggregate and therefore more dangerous to the cells, but i'm not expressing these in anything anyways, so i still think it would be nice to have a good-looking image.

predicted protein structure:

cartoon representation

surface representation

[mindblowingscience]

Scientists in Canada and the U.S. have discovered a new way in which Ebola—an often deadly virus affecting people mostly in sub-Saharan Africa—reproduces in the body. By shedding light on how the virus interacts with a human protein called ubiquitin, the researchers have also identified a potential target for new drugs to prevent the disease.

Continue Reading.

[humancelltournament]

Propaganda!

Podocytes are cells in Bowman's capsule in the kidneys that wrap around capillaries of the glomerulus. Podocytes filter the blood, retaining large molecules such as proteins while smaller molecules such as water, salts, and sugars are filtered as the first step in the formation of urine.

SUMO (Small Ubiquitin-like Modifier) proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function, via a process is called SUMOylation. SUMOylation is a post-translational modification involved in various cellular processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle.

[longhaulerbear]

Several of the most prevalent new-onset autoantibodies have, to our knowledge, not been described previously, including the three with the highest prevalence, i.e., anti-CCDC63 (coiled-coil domain-containing protein 63), anti-TRIM63 (E3 ubiquitin-protein ligase TRIM63), and anti-SNURF (SNRPN upstream reading frame protein)

[whats-in-a-sentence]

Strigolactones are perceived by a protein complex containing an α-/β-fold hydrolase protein and an F-box protein (D14 end MAX2, respectively) (Figure 19.31).

"Plant Physiology and Development" int'l 6e - Taiz, L., Zeiger, E., Møller, I.M., Murphy, A.

[tenth-sentence]

In brief, a small protein called ubiquitin is first activated by an enzyme termed an E1 ubiquitin-activating enzyme in an ATP-dependent manner (Figure 15.33A; see also Figure 2.18).

"Plant Physiology and Development" int'l 6e - Taiz, L., Zeiger, E., Møller, I.M., Murphy, A.

[maxinemartinsdrill]

got too into iwtv and now I'm learning about the ubiquitin - proteasome pathway

[er-cryptid]

26S Proteasome

-- protein complex

-- found in eukaryotes

-- large

-- cylindrical

-- degrades ubiquitin-labeled proteins in peptides

.

Patreon

[castingcomets]

In my senior year of highschool we had a final project in AP Biology which was open-ended and could be just about anything. I rewrote (and performed) Thrift Shop to be about various branches of biology using the terminology that we had used that year. I titled it "Niche Shop."

These are the lyrics.

^ So you can follow along.

Hey… You wanna go niche shopping?

I’m an organism I’m alive You can tell by how all my cells utilize I’m- I’m- I’m growing, adapting and I’m showing, This is my response

Walk into a niche like what up I’m an organism Organ cells, organelles, carbon-based organ systems If I’m surviving, got the traits you wanna copy Got ‘em like- “Damn, I better acquire mimicry”

Factor in, fitness my kin Nat select me as a king Dressed as a warning or I’m camouflaged from everything The strongest or the fastest, sharper than Damascus But if you really wanna live, you gotta have looooong… Telomeres!

Hoofin’ it, wingin’ it, gonna optimal forage it Passin’ up through the TD forest Humus is a freebie nourish Not rockin’ semelparity but, I am a rarity 1.8 meters too much room for a disparity!

An issue of polarity, Irregularity of molarity, Disrupts cellular activity Lacking biologic dexterity

Dehydration synthesis, poly or di Covalent bonding with all the mama-saccharides!

They had an H ion, I took an H ion For ETC so I can have the energy to hang on Mito makes a maze of its membranes To gain energy used in transduction signal pathway chains

I could take some bases, Rough ‘em up and misplace The wild types would be like “Oh, he got the lactase”

I’m gonna eat some carbs I need energy and I’m on guard I’m- I’m- I’m drinking, drying and I’m linking, This is glycosidic

I’m gonna bond some peptides There are four structures so please stay wise I’m- I’m- I’m asking, amino group and acid, But don’t forget nucleotides (AUOHW!!)

What’chu know about being hydrophobic? What’chu know about being hydrophilic? I’m diffusion’, I’m movin’ right through that fatty bilayer Meet the mosaic and all its necessary players!

Thank Aunt Ester, for linking glycerols and fatty acids It’s an asset keep ‘em like molasses Metabolism, you can have in catabolic (bolic) Minus delta G or you can have it anabolic (bolic)

Prokaryotes, no nucleus All have membranes like eukaryotes Cyto-structure and ribosomes and DNA in that cytoplasm Eukaryotes have organelles in that cytoplasm Lysosomes and vacuoles in that cytoplasm

They’re like “oh, that peroxisome, that’s hella tight” I’m like “yo… that makes hydrogen peroxide” Competitive inhibition will render us quickly illin’ Catalyse that catalase to cure our condition

Don’t forget, ‘bout the mosaic composition Don’t forget, about what lets somethin’ else in That receptor is hella though But havin’ a common one in a pandemic is a hella NO

Peep gang, come take a look at my DNA Find all the nights I spent with retroviral RNA

[Interlude] In your DNA … viral RNA … turned to DNA … and then to RNA Immune … poppin’ cells … yeah!

I’m gonna place some tags Ubiquitin be quittin’ on all these proteins This cellular machine, RNA in vaccines An acid for every codon

I made God to be in my image All these kids descend from my lineage I have eternal DNA My fitness is secured through advantageous traits [X2]

As DNA replicates Every cell from a cell - this never dates I’m- I’m- I’m growing, adapting and I’m showing, This is my response

Are those your Grandpa’s genes?